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Plant tissue in vitro culture is increasingly used in agriculture to improve crop production, nutritional quality, and commercial value. In plant virology, the technique is used as sanitation protocol to produce virus‐free plants. Sanitized (S) artichokes show increased vigour compared to their non‐sanitized (NS) counterparts, because viral infections lead to a decline of growth and development.To investigate mechanisms that control the complex traits related to morphology, growth, and yield in S artichokes compared to NS plants, RNAseq analysis and phenotyping by imaging were used. The role of peroxidases (POD) was also investigated to understand their involvement in sanitized plant development.Results showed that virus infection affected regulation of cell cycle, gene expression and signal transduction modulating cellular response to stimulus/stress. Moreover, primary metabolism and photosynthesis were also influenced, contributing to explain the main morphological differences observed between S and NS artichokes. Sanitized artichokes are also characterized by higher POD activity, probably associated with increased plant growth, rather than strengthening of cell walls.Overall, results show that the differences in development of S artichokes may be derived from the in vitro culture stressor, as well as through pathogen elimination, which, in turn, improve qualitative and quantitative artichoke production. [ABSTRACT FROM AUTHOR]